Biology subjects

Foley, M.

Publications and source records attributed to Foley, M..

9 recordsLinked to original sources

bioRxiv2026

Reduced skeletal density and mechanical resistance in mangrove-associated Pocillopora sp. corals

Coral skeletal integrity underpins reef habitat complexity and coastal protection, yet it remains unclear whether corals persisting in chemically variable marginal habitats, such as mangrove-associated reefs, maintain sufficient mechanical resistance to withstand physical disturbance. We combined micro-computed tomography (micro-CT) morphometric analysis with compression testing to quantify skeletal microarchitecture and compressive mechanical performance of Pocillopora sp. skeletons collected across a habitat gradient at Low Isles, Great Barrier Reef, from mangrove-associated sites to exposed reef sites. Baseline skeletal properties varied among sites, with the Proximal Reef site having the densest and least porous skeletons, while mangrove-associated sites had the most porous skeletons. Similarly, Proximal Reef skeletons exhibited two-to-three-fold greater compressive stiffness and peak force than mangrove-associated skeletons. Percentage object volume was a stronger predictor of compressive stiffness than surface area-to-volume (S/V) ratio, indicating that bulk skeletal density better captured load-bearing capacity than surface architectural complexity. Structural failure mode also differed markedly among habitats: mangrove-associated skeletons underwent catastrophic fragmentation of their open, porous framework, whereas Distal and Proximal Reef skeletons failed through discrete crack-plane propagation while largely maintaining overall structural coherence. These results indicate that the physiological stress tolerance associated with mangrove habitats occurs alongside reduced mechanical resistance and more destructive failure modes, suggesting a potential trade-off between chemical stress tolerance and structural investment. Assessments of resilience in marginal coral populations should therefore consider skeletal mechanical performance alongside physiological tolerance, particularly as climate change intensifies storms and alters hydrodynamic disturbance regimes.

ecology↗

bioRxiv2025

Drought reduces formation, but enhances persistence, of mineral-associated organic matter in a grassland soil

Drought effects are pervasive in many terrestrial ecosystems, yet little is known about the impact of drought on the transformation of plant C inputs to mineral-associated organic matter (MAOM) - the largest and slowest-cycling pool of organic carbon (C) on land. Using 13C-CO2 greenhouse labeling chambers, we tracked the formation of 13C-MAOM derived from Avena barbata living root inputs (13C-rhizodeposits) versus A. barbata decaying root inputs (13C-root detritus) under normal moisture and spring drought conditions in a semi-arid grassland soil, and then tested the durability of this 13C-MAOM in a subsequent persistence assay. Overall, drought reduced formation of MAOM - both per gram of soil and across the entire soil profile. Notably, drought conditions enhanced the persistence of MAOM derived from root detritus, though not of MAOM derived from rhizodeposition. Drought had the most pronounced effect on MAOM accrual from rhizodeposition late in plant development (week 12) whereas it had the most pronounced effect on MAOM accrual from root detritus early in root decomposition (week 4). These temporal responses were associated with distinct trajectories in microbial community-level growth rates, the average mass of OM compounds, and the number of unique metabolites within each habitat. Our results provide mechanistic evidence that drought reduces overall formation of MAOM but can enhance its persistence in a grassland soil.

ecology↗

bioRxiv2025

Specialist Generalist Trade Offs in Microbial Growth Rates Across Soil Habitats

Microbial ecological strategies are shaped by a fundamental trade-off: is it better to specialize and thrive in a narrow niche or generalize and persist across diverse environments? In soils, this trade-off is particularly relevant in the rhizosphere and detritusphere, where microorganisms encounter distinct resource inputs from living and decaying roots. Using H {superscript 1} O quantitative stable isotope probing (qSIP), we measured in situ bacterial and fungal growth rates in the rhizosphere, the root detritusphere, and in the combined presence of rhizosphere + root detritus to test whether specialists--microbes growing in a single habitat--grow faster than generalists that persist across multiple environments. Specialists grew consistently faster than generalists, suggesting a trade-off between the breadth of environmental conditions a microorganism can tolerate and its ability to grow quickly in a specific habitat. This cost to broad niche adaptation was apparent for bacteria, but growth rates of fungal saprotrophs varied little between specialists and generalists, reflecting how fundamental differences in life-history strategies between bacteria and fungi can shape microbial responses to resource availability and habitat heterogeneity. Net relatedness and nearest taxon indices indicated total bacterial communities were phylogenetically clustered while specialist and generalist communities were phylogenetically random, suggesting that functional traits, not lineage, best predict ecological strategy. In annual grassland soils, fast-growing specialists may dominate ecosystem processes when resources abound, and slow-growing generalists may sustain element transformations when conditions shift; understanding this interplay is key to predicting soil-carbon trajectories.

microbiology↗

bioRxiv2025

Composition, growth, succession, and function in the Cladophora microbiome: insights from quantitative Stable Isotope Probing and NanoSIMS imaging

The branching green macroalga Cladophora glomerata and its epiphytic microbiome dominate summer biomass in the Eel River, a Northern California river under Mediterranean (summer drought, winter rain) seasonality. Green Cladophora streamers proliferate in early summer, then change to yellow and then red-brown as epiphyte loads increase. We characterized successional changes in epiphytic bacteria on Cladophora, examining both community composition and growth rates, using quantitative Stable Isotope Probing (qSIP) and16S rRNA gene amplicon sequencing. The number of bacterial taxa increased with succession while growth rates peaked in the middle stage. NanoSIMS imaging confirmed high sulfur (S) concentrations in Cladophora cell walls relative to surrounding biomass, coinciding with a bloom of sulfur bacteria (bacteria that reduce or oxidize sulfur/sulfates). In general, relative abundances and growth rates were independent, indicating that either metric alone is insufficient for understanding how taxonomy and functional groups affect ecosystem processes. For instance, the relative abundance of nitrogen fixers peaked in the late summer when their relative growth rates were slowest. Such patterns may be driven by space competition limiting growth. Together, changes in abundance and relative growth rates suggest different limiting factors for different functional groups in the Cladophora microbiome at multiple successional stages.

microbiology↗

bioRxiv2025

An abundant merozoite surface protein of Plasmodium falciparum modulates susceptibility to inhibitory antibodies

Malaria merozoite surface proteins (MSPs), are thought to have important roles in red blood cell (RBC) invasion and their exposure on the parasite surface makes them attractive vaccine candidates. However, their role in invasion has not been directly demonstrated and their biological functions are unknown. One of the most abundant proteins is PfMSP2, which is likely an ancestral protein that has been maintained in the Plasmodium falciparum lineage and is a focus of vaccine development, whose function remains unknown. Using CRISPR-Cas9 gene-editing, we removed PfMSP2 from two different P. falciparum lines with no impact on parasite replication or phenotype in vitro, demonstrating that it is not essential for RBC invasion. However, loss of PfMSP2 led to increased inhibitory potency of antibodies targeting other merozoite proteins involved in invasion, particularly PfAMA1. In a solid-phase model, increasing concentrations of PfMSP2 protein reduced binding of different antibodies against PfAMA1 in a dose dependent manner. These data suggest that PfMSP2 can modulate the susceptibility of merozoites to protective inhibitory antibodies. The results of this study change our understanding of the potential functions of PfMSP2 and establishes a new concept in malaria where a surface protein can reduce the protective efficacy of antibodies targeting a different antigen. These findings have important implications for understanding malaria immunity and informing vaccine development.

microbiology↗

bioRxiv2025

Total body irradiation primes CD19-directed CAR T cells against large B-cell lymphoma

CD19-targeting chimeric antigen receptor T cells (CART19) have demonstrated significant effectiveness in treating relapsed or refractory large B-cell lymphoma (LBCL). However, they often fail to sustain durable remissions in more than half of all treated patients. Therefore, there is an urgent need to identify approaches to enhance CART19 efficacy. Here, we studied the impact of low-dose radiation on CART19 activity in vitro and find that radiation enhances the cytotoxicity of CART19 against LBCL by upregulating death receptors. Disrupting the FAS receptor diminishes this benefit, indicating that this pathway plays an important role in enhancing the cytotoxic effects of CAR T cells. To further validate these findings, we conducted in vivo studies using a lymphoma syngeneic mouse model delivering total body irradiation (TBI). We observed that delivering TBI at a single dose of 1Gy prior to CAR T cell infusion significantly improved CART19-mediated tumor elimination and increased overall survival rates. Importantly, we characterized several important effects of TBI, including enhanced lymphodepletion, improved T cell expansion and persistence, better intra-tumoral migration, and a more favorable, anti-tumor phenotypic composition of the T cells. In summary, for the first time, we have demonstrated preclinically that administering TBI before CART19 infusion significantly accelerates tumor elimination and improves overall survival. This approach holds promise for translation into clinical practice and serves as a valuable foundation for further research to enhance outcomes for patients receiving CART19 treatment.

cancer biology↗

bioRxiv2022

Neural noise is associated with age-related neural dedifferentiation

Age-related neural dedifferentiation - reductions in the selectivity and precision of neural representations - contributes to cognitive aging and is thought to result from age increases in neural noise. This research has primarily used fMRI to examine age-related reductions in neural selectivity for different categories of visual stimuli. The present experiment used EEG to examine the link between neural noise and age-related neural dedifferentiation indexed by the scene-selective (P200) and face-selective (N170) ERP components. Young and older adults viewed images of scenes, objects, and faces during a 1-back task. Whereas both the P200 and N170 showed age-related slowing of peak latency, only the P200 showed age-related reductions in amplitude that were independent of visual and contrast acuity. We also examined the relationship between the ERP peak measures and an index of neural noise, namely the 1/f exponent of the frequency power spectrum. For the P200 amplitude, higher levels of neural noise were associated with smaller P200 amplitudes in young, but not older adults. In contrast, there was an age-invariant relationship between neural noise and N170 amplitude in the left hemisphere with higher levels of neural noise being associated reduced N170 amplitudes. While the present findings provide novel empirical evidence broadly consistent with predictions from computational models of neural dedifferentiation, the results also highlight potential limitations of the computational model that necessitate revision. The results also suggest that, at least for the P200, maintaining levels of neural noise similar to young adults might preserve levels of neural selectivity. Significance StatementA prominent theory of cognitive aging proposes that age-related cognitive decline results from increases in neural noise that reduce the selectivity of neural representations. We examined this predicted link between neural selectivity and neural noise with ERP components that show selectivity for scenes (P200) and faces (N170) and the 1/f aperiodic exponent measure of neural noise. The amplitude for the scene-selective, but not face-selective, ERP component was reduced in older adults, with both components showing age-related slowing. Critically, older adults with higher levels of neural noise showed lower levels of neural selectivity for scenes, but not faces. While these results provide some evidence supporting computational models of neural dedifferentiation, they also highlight important limitations of the model that require revision.

neuroscience↗

bioRxiv2022

Divergent microbial traits influence the transformation of living versus dead root inputs to soil carbon

Soil microorganisms influence the global carbon cycle by transforming plant inputs into soil organic carbon (SOC), but the microbial traits that facilitate this process are unresolved. While current theory and biogeochemical models suggest microbial carbon-use efficiency and growth rate are positive predictors of SOC, recent observations demonstrate these relationships can be positive, negative, or neutral. To parse these contradictory effects, we used a 13C-labeling experiment to test whether different microbial traits influenced the transformation of plant C into SOC within the microbial habitats surrounding living root inputs (rhizosphere) versus decaying root litter (detritusphere), under both normal soil moisture and droughted conditions. In the rhizosphere, bacterial-dominated communities with fast growth, high carbon-use efficiency, and high production of extracellular polymeric substances formed microbial-derived SOC under normal moisture conditions. However, in the detritusphere - and the rhizosphere under drought - more fungal-dominated communities with slower growth but higher exoenzyme activity formed plant-derived SOC. These findings emphasize that microbial traits linked with SOC accrual are not universal, but contingent on how microorganisms allocate carbon under different resource conditions and environmental stressors.

ecology↗

bioRxiv2021

Male sex and age biases viral burden, viral shedding, and type 1 and 2 interferon responses during SARS-CoV-2 infection in ferrets

SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) hospitalizations and deaths disportionally affect males and the elderly. Here we investigated the impact of male sex and age by infecting adult male, aged male, and adult female ferrets with SARS-CoV-2. Aged male ferrets had a decrease in temperature which was accompanied by prolonged viral replication with increased pathology in the upper respiratory tract after infection. Transcriptome analysis of the nasal turbinates and lungs indicated that female ferrets had significant increases in interferon response genes (OASL, MX1, ISG15, etc.) on day 2 post infection which was delayed in aged males. In addition, genes associated with taste and smell such as RTP1, CHGA, and CHGA1 at later time points were upregulated in males but not in females. These results provide insight into COVID-19 and suggests that older males may play a role in viral transmission due to decreased antiviral responses.

microbiology↗